| Matrix | base class for matrix patterns, containing methods common
to all |
| MatrixSet | an agregate class representing a set of matrix patterns, containing methods for manipulating the set as a whole |
| PatternGen | a base class for pattern generators |
| PatternI | interface definition for all pattern objects (currently
includes matrices and word (consensus and regular expressions ) |
| Site | a nucleotide sequence feature object representing (possibly putative) transcription factor binding site. |
| SitePairSet | a set of TFBS::SitePair objects |
| SiteSet | a set of TFBS::Site objects |
| Word | base class for word-based patterns |